BioC 3.1: CHECK report for metagenomeSeq on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘metagenomeSeq’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘biom’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/30s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [9s/9s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/metagenomeSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘metagenomeSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘metagenomeSeq’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘metagenomeSeq’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘metagenomeSeq’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘metagenomeSeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metagenomeSeq)

name	user	system	elapsed
MRcoefs	0.997	0.028	1.025
MRcounts	0.304	0.019	0.323
MRexperiment-class	0	0	0
MRfulltable	0.855	0.030	3.005
MRtable	0.942	0.016	0.961
aggregateBySample	0.169	0.012	0.181
aggregateByTaxonomy	0.173	0.000	0.172
biom2MRexperiment	0.000	0.000	0.001
calcNormFactors	0.641	0.020	0.662
correctIndices	0.120	0.000	0.121
correlationTest	0.247	0.011	0.255
cumNorm	0.699	0.001	0.702
cumNormMat	0.662	0.000	0.663
cumNormStat	1.032	0.019	1.053
cumNormStatFast	0.416	0.004	0.420
expSummary	0.105	0.008	0.112
exportMat	0.000	0.000	0.001
exportStats	0	0	0
filterData	0.189	0.007	0.197
fitDO	0.567	0.018	2.083
fitPA	0.539	0.026	1.881
fitSSTimeSeries	1.288	0.016	1.303
fitTimeSeries	1.280	0.016	1.299
fitZig	2.633	0.028	2.728
libSize	0.322	0.011	0.334
load_biom	0.000	0.000	0.001
load_meta	0.029	0.000	0.028
load_metaQ	0.000	0.000	0.001
load_phenoData	0.001	0.000	0.000
newMRexperiment	0.039	0.000	0.040
normFactors	0.321	0.008	0.330
plotBubble	0.527	0.015	1.821
plotClassTimeSeries	1.255	0.012	1.284
plotCorr	0.739	0.008	0.747
plotFeature	0.170	0.000	0.172
plotGenus	0.178	0.000	0.179
plotMRheatmap	2.318	0.000	2.329
plotOTU	0.180	0.004	0.185
plotOrd	0.358	0.000	0.357
plotRare	0.127	0.004	0.131
plotTimeSeries	1.127	0.004	1.148
posteriorProbs	0.001	0.000	0.001
returnAppropriateObj	0.322	0.004	0.335
ssFit	0	0	0
ssIntervalCandidate	0	0	0
ssPerm	0.000	0.000	0.001
ssPermAnalysis	0.001	0.000	0.003
trapz	0.001	0.000	0.001
uniqueFeatures	0.136	0.000	0.144
zigControl	0	0	0

BioC 3.1: CHECK report for metagenomeSeq on zin2

Summary

Command output